+#!/usr/bin/perl
+
+package rsem_perl_utils;
+
+use strict;
+
+require Exporter;
+our @ISA = qw(Exporter);
+our @EXPORT = qw(runCommand);
+our @EXPORT_OK = qw(runCommand collectResults showVersionInfo);
+
+# command, {err_msg}
+sub runCommand {
+ print $_[0]."\n";
+ my $status = system($_[0]);
+
+ if ($? == -1) {
+ my @arr = split(/[ \t]+/, $_[0]);
+ print "$arr[0] : $!!\n";
+ print "Please check if you have compiled the associated codes by typing related \"make\" commands and/or made related executables ready to use.\n";
+ exit(-1);
+ }
+
+ if ($status != 0) {
+ my $errmsg = "";
+ if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
+ $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
+ print $errmsg;
+ exit(-1);
+ }
+ print "\n";
+}
+
+
+my @transcript_title = ("transcript_id", "gene_id", "length", "effective_length", "expected_count", "TPM", "FPKM", "IsoPct", "pme_expected_count", "pme_TPM", "pme_FPKM", "IsoPct_from_pme_TPM", "TPM_ci_lower_bound", "TPM_ci_upper_bound", "FPKM_ci_lower_bound", "FPKM_ci_upper_bound");
+
+my @gene_title = ("gene_id", "transcript_id(s)", "length", "effective_length", "expected_count", "TPM", "FPKM", "pme_expected_count", "pme_TPM", "pme_FPKM", "TPM_ci_lower_bound", "TPM_ci_upper_bound", "FPKM_ci_lower_bound", "FPKM_ci_upper_bound");
+
+# inpF, outF
+sub collectResults {
+ my $local_status;
+ my ($inpF, $outF);
+ my @results = ();
+ my $line;
+
+ $inpF = $_[1];
+ $outF = $_[2];
+
+ $local_status = open(INPUT, $inpF);
+ if ($local_status == 0) { print "Fail to open file $inpF!\n"; exit(-1); }
+
+ @results = ();
+
+ while ($line = <INPUT>) {
+ chomp($line);
+ my @local_arr = split(/\t/, $line);
+ push(@results, \@local_arr);
+ }
+
+ close(INPUT);
+
+ $local_status = open(OUTPUT, ">$outF");
+ if ($local_status == 0) { print "Fail to create file $outF!\n"; exit(-1); }
+
+ my $n = scalar(@results);
+ my $m = scalar(@{$results[0]});
+
+ $" = "\t";
+
+ my @out_arr = ();
+ for (my $i = 0; $i < $n; $i++) {
+ if ($_[0] eq "isoform") { push(@out_arr, $transcript_title[$i]); }
+ elsif ($_[0] eq "gene") { push(@out_arr, $gene_title[$i]); }
+ else { print "A bug on 'collectResults' is detected!\n"; exit(-1); }
+ }
+ print OUTPUT "@out_arr\n";
+
+ for (my $i = 0; $i < $m; $i++) {
+ @out_arr = ();
+ for (my $j = 0; $j < $n; $j++) { push(@out_arr, $results[$j][$i]); }
+ print OUTPUT "@out_arr\n";
+ }
+
+ close(OUTPUT);
+}
+
+# dir
+sub showVersionInfo {
+ open(INPUT, "$_[0]\WHAT_IS_NEW");
+ my $line = <INPUT>;
+ chomp($line);
+ close(INPUT);
+ print "$line\n";
+ exit(0);
+}
+
+1;